The conformation of bound GMPPNP suggests a mechanism for gating  the active site of the SRP GTPase  (2001) Padmanabhan, S. & Freymann, D.M.  Structure   9  859-867.

Abstract

Background:  The signal recognition particle (SRP) is a phylogenetically conserved ribonucleoprotein that mediates co-translational targeting of secreted and membrane proteins to the membrane. Targeting is regulated by GTP binding and hydrolysis events that require the direct interaction between structurally homologous 'NG' GTPase domains of the SRP signal recognition subunit and its membrane-associated receptor, SRa.  Structures of both the apo and GDP-bound NG domains of the prokaryotic SRP54 homolog, Ffh, and the prokaryotic receptor homolog, FtsY, have been determined.  The structural basis for the GTP-dependent interaction between the two proteins, however, remains unknown.  

Results:  We report here two structures of the NG GTPase of Ffh from Thermus aquaticus bound to the non-hydrolyzable GTP analog GMPPNP.  Both structures reveal an unexpected binding mode in which the b-phosphate is kinked away from the binding site and magnesium ion is not bound.  Binding of the GTP analog in the canonical conformation found in other GTPase structures is precluded by constriction of the phosphate binding P-loop.  The structural difference between the Ffh complex and other GTPases suggests a specific conformational change that must accompany movement of nucleotide from an 'inactive' to an 'active' binding mode.

Conclusions:  Conserved sidechains of the GTPase sequence motifs unique to the SRP subfamily may function to gate formation of the ‘active’ GTP-bound conformation.  Exposed hydrophobic residues provide an interaction surface that may allow regulation of the GTP binding conformation, and thus activation of the GTPase, during association of SRP with its receptor.

Pubmed

PDB: 1JPN  1JPJ

Comment
One of the first steps in understanding a GTPase is to determine how it responds to binding nucleotide.  This structure was a surprise - we obtained two different crystal forms that revealed the GTP analog GMPPNP bound in a configuration that allowed the protein conformation to remain the same as the unbound state.  The result was really puzzling, although it did seem to be consistent with the behavior observed in biochemical studies of the eukaryotic SRP and receptor that suggested that, contrary to the behavior of other GTPases, the empty state (or non-activated state) was functionally significant for the SRP.

Some relevent references include:

Rapiejko PJ & Gilmore R (1997) "Empty site forms of the SRP54 and SR alpha GTPases mediate targeting of ribosome-nascent chain complexes to the endoplasmic reticulum" Cell 89 703-13.

Lu Y, Qi H-Y,Hyndman JB, Ulbrandt ND, Teplyakov A, Tomasevic N, Bernstein HD (2001) "Evidence for a novel GTPase priming step in the SRP protein targeting pathway" The EMBO Journal 20, 6724–6734

Song W., Raden,D., Mandon,E.C. and Gilmore,R. (2000) Role of Sec61α in the regulated transfer of the ribosome–nascent chain complex from the signal recognition particle to the translocation channel. Cell, 100, 333–343.

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